The percentage of oropharyngeal cancers associated with HPV16 infection rose from 16.3% between the years of 1984 to 1989 to 71.7% between the years of 2000 to 2004. In contrast, the number of tobacco-related oropharyngeal cancers has been steadily declining over the same time period. Similar changes have been reported in multiple countries. There have been substantial changes in the burden of cancer affecting HIV- infected individuals in the U.S. during a 12-year period spanning the introduction of highly active anti-retroviral therapy (HAART). Among these emerging malignancies, HPV-associated cancers of the oral cavity/pharynx increased significantly following an AIDS diagnosis. HPV is rapidly changing the landscape of HNSCC. However, the mechanisms and natural history of oral HPV infection and oncogenic progression is poorly understood. Extrapolation of knowledge of HPV-associated oncogenicity in the genital tract is not satisfactory to our understanding of oral HPV disease. HPV is necessary, but not sufficient cause of invasive cervical cancer. The epigenetic mark of methylation is a common hallmark of human cancer. Epigenetic studies using the proper model systems can provide significant increases in our knowledge concerning the mechanisms and signaling pathways that drive HPV infection, life cycle, and oncogenesis. Aberrant microRNAs (miRNAs) expression is becoming recognized as a new molecular mechanism of carcinogenesis. HPV-infected keratinocytes express a different set of miRNAs when compared to noninfected keratinocytes. Additionally, HPV-infected cells grown in nondifferentiating monolayer culture express a different set of miRNAs compared to HPV-infected differentiating keratinocytes. Our long-term goal is to investigate the epigenetic mechanisms of HPV-associated oral disease. HPV16 is associated with 90-95% of HNSCC. Our studies will focus on HPV16. Our hypothesis is that the effect of the HPV life cycle and carcinogenesis on the epigenomic landscape of oral epithelium is further affected by HIV antiretroviral therapy (ART). The epigenome of both the host genome and the viral genome is affected. A combination of next generation sequencing analysis of the methylome and co-altered miRNA expression will be used to identify epigenetic modifications of high importance. We will test these hypotheses in three specific aims SPECIFIC AIM 1: Measure genome-wide epigenetic changes occurring at different stages of the HPV16 life cycle. SPECIFIC AIM 2: Measure genome-wide epigenetic changes occurring during HPV16 carcinogenic progression. SPECIFIC AIM 3: Delineate epigenetic modifications that occur in response to ART treatment.